I was communicating with Kobo about a similar issue recently; for me, it was the "thin space" character, which is used in some books between a single and double quote mark in a nested quotation. I found that the thin space character was present in the built in font Rakuten Serif, but not in Kobo Nickel. If I set RS as primary and KN as secondary, it displayed correctly. However, if I set KN as primary and RS as secondary, I get a box symbol instead.
Here was the conclusion to my chat:
Quote:
The “Supplemental font” is meant to provide glyph fallback when your chosen font doesn’t include certain characters (for example, mixing Latin text with occasional CJK or symbols). In the current firmware, however, that fallback doesn’t consistently apply to certain Unicode space characters like THIN SPACE (U+2009). Those spaces are handled differently by the layout engine, so when the primary font lacks the glyph, the device can show a missing‑glyph box instead of drawing it from the supplemental font. That’s why Nickel as primary + Rakuten Serif as supplemental still shows the box.
It is not a bug but its something definitely we can take feedback to improve in the future,
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I don't know which characters you were missing, but maybe they fall into the same hole.